VIII. Don't connect all of your amplifier ground wires under one bolt. Contrary to belief, this is not required if the rest of the system is installed properly. If you do connect more than one power ground wire under a single bolt, you run the risk of amplifier ground modulation. This is caused by the current demands of, for example a woofer amp, modulating the power ground wire of a tweeter amp. This results in a squeaking noise that can be heard over the tweeters whenever bass notes hit.
http://www.termpro.com/articles/noise.html
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Is it a RPM whine?
If it was me, Id crimp both grounds together, lose that junction box dealio, and Ground loop thing... and bolt on 2shorty wires in the trunk.
Then, Id check my power wire and spark plug wires. and make sure its not close to the coilpack or plugs...
Then, If still there, Id disconnect the Sub amp completely, and see if noise still there with just the kicker powered.
If still there, Id disconnect the Sub RCA's from the deck and amp.
Or, Id turn off the Sub Out from the pioneer if you can defeat it.
If still there, its the Kicker amp wiring thats bad Id say eh? or vice versa?
Where do you have the ground bolt on your install at? I grounded mine real close to the left of the spare tire well.